{"doi":"10.7554/elife.67236","title":"High-resolution, genome-wide mapping of positive supercoiling in chromosomes","abstract":"Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to Escherichia coli and Saccharomyces cerevisiae , we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently oriented genes, consistent with the ‘twin-domain’ model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin-binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.","journal":"eLife","year":2021,"id":150900,"datarank":2.490078618608453,"base_score":4.48863636973214,"endowment":4.48863636973214,"self_citation_contribution":0.6732954554598211,"citation_network_contribution":1.8167831631486318,"self_endowment_contribution":0.6732954554598211,"citer_contribution":1.8167831631486318,"corpus_percentile":null,"corpus_rank":null,"citation_count":88,"citer_count":82,"citers_with_citation_signal":70,"citers_with_endowment":70,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9443,"is_data_producer":true,"deposit_databanks":{"GEO":["GSE152882","GSM2690550","GSM3668254","GSM3069971","GSM1705337","GSM3141352"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":641672,"name":"Ryo Kawamura","orcid":null,"position":1,"is_corresponding":false},{"id":297688,"name":"Megan L. Littlehale","orcid":"0000-0002-6848-5687","position":2,"is_corresponding":false},{"id":254911,"name":"John F. Marko","orcid":"0000-0003-4151-9530","position":3,"is_corresponding":false},{"id":21271,"name":"Michael T. Laub","orcid":"0000-0002-8288-7607","position":4,"is_corresponding":false},{"id":297689,"name":"Monica S. Guo","orcid":"0000-0002-6720-2323","position":0,"is_corresponding":true}],"reference_count":87,"raw_metadata":null,"created_at":"2026-07-18T23:43:06.501849Z","pmid":"34279217","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}